BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 007865
         (587 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3PSI|A Chain A, Crystal Structure Of The Spt6 Core Domain From
           Saccharomyces Cerevisiae, Form Spt6(239-1451)
          Length = 1219

 Score = 28.9 bits (63), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 46/97 (47%), Gaps = 8/97 (8%)

Query: 253 LNKCFYECHDETEFQVSWDDMINKFSLGDHLWLKKLYSLRDKWCLVFNSDTFSANIDSVQ 312
           ++K F   +D TEF+ +  + I KF   ++L +  +Y+ R  +      D F    D + 
Sbjct: 125 VDKNFDANYDLTEFKEAIGNAI-KFITKENLEVPFIYAYRRNYISSREKDGFLLTEDDLW 183

Query: 313 RSDSIDTVFHQVSTKRMDVISFVQHFEEKTKEMHLDE 349
              S+D  FH +  K+     +VQ F     E+H+D+
Sbjct: 184 DIVSLDIEFHSLVNKK----DYVQRF---YAELHIDD 213


>pdb|3PSF|A Chain A, Crystal Structure Of The Spt6 Core Domain From
           Saccharomyces Cerevisiae, Form Spt6(236-1259)
          Length = 1030

 Score = 28.9 bits (63), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 46/97 (47%), Gaps = 8/97 (8%)

Query: 253 LNKCFYECHDETEFQVSWDDMINKFSLGDHLWLKKLYSLRDKWCLVFNSDTFSANIDSVQ 312
           ++K F   +D TEF+ +  + I KF   ++L +  +Y+ R  +      D F    D + 
Sbjct: 128 VDKNFDANYDLTEFKEAIGNAI-KFITKENLEVPFIYAYRRNYISSREKDGFLLTEDDLW 186

Query: 313 RSDSIDTVFHQVSTKRMDVISFVQHFEEKTKEMHLDE 349
              S+D  FH +  K+     +VQ F     E+H+D+
Sbjct: 187 DIVSLDIEFHSLVNKK----DYVQRF---YAELHIDD 216


>pdb|4EQ5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sibiricus
          Length = 571

 Score = 28.5 bits (62), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 27/60 (45%), Gaps = 10/60 (16%)

Query: 37  KIFEASGGVDVGRRRTKPLSYLGNDFGGDRNVQFAKKDMGNYLPREMGNMMEPGDVQGLL 96
           KI EASG     R+    L YL N F        A  D G YL R +  +M  G  +GLL
Sbjct: 134 KIAEASGAGSQDRK----LKYLANLF------MDASPDEGKYLARTVLGIMRTGVAEGLL 183


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.322    0.135    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,849,109
Number of Sequences: 62578
Number of extensions: 673621
Number of successful extensions: 1202
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1202
Number of HSP's gapped (non-prelim): 3
length of query: 587
length of database: 14,973,337
effective HSP length: 104
effective length of query: 483
effective length of database: 8,465,225
effective search space: 4088703675
effective search space used: 4088703675
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)